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Accounts of Chemical Research Mar 2018Electrode technology for electrophysiology has a long history of innovation, with some decisive steps including the development of the voltage-clamp measurement... (Review)
Review
Electrode technology for electrophysiology has a long history of innovation, with some decisive steps including the development of the voltage-clamp measurement technique by Hodgkin and Huxley in the 1940s and the invention of the patch clamp electrode by Neher and Sakmann in the 1970s. The high-precision intracellular recording enabled by the patch clamp electrode has since been a gold standard in studying the fundamental cellular processes underlying the electrical activities of neurons and other excitable cells. One logical next step would then be to parallelize these intracellular electrodes, since simultaneous intracellular recording from a large number of cells will benefit the study of complex neuronal networks and will increase the throughput of electrophysiological screening from basic neurobiology laboratories to the pharmaceutical industry. Patch clamp electrodes, however, are not built for parallelization; as for now, only ∼10 patch measurements in parallel are possible. It has long been envisioned that nanoscale electrodes may help meet this challenge. First, nanoscale electrodes were shown to enable intracellular access. Second, because their size scale is within the normal reach of the standard top-down fabrication, the nanoelectrodes can be scaled into a large array for parallelization. Third, such a nanoelectrode array can be monolithically integrated with complementary metal-oxide semiconductor (CMOS) electronics to facilitate the large array operation and the recording of the signals from a massive number of cells. These are some of the central ideas that have motivated the research activity into nanoelectrode electrophysiology, and these past years have seen fruitful developments. This Account aims to synthesize these findings so as to provide a useful reference. Summing up from the recent studies, we will first elucidate the morphology and associated electrical properties of the interface between a nanoelectrode and a cellular membrane, clarifying how the nanoelectrode attains intracellular access. This understanding will be translated into a circuit model for the nanobio interface, which we will then use to lay out the strategies for improving the interface. The intracellular interface of the nanoelectrode is currently inferior to that of the patch clamp electrode; reaching this benchmark will be an exciting challenge that involves optimization of electrode geometries, materials, chemical modifications, electroporation protocols, and recording/stimulation electronics, as we describe in the Account. Another important theme of this Account, beyond the optimization of the individual nanoelectrode-cell interface, is the scalability of the nanoscale electrodes. We will discuss this theme using a recent development from our groups as an example, where an array of ca. 1000 nanoelectrode pixels fabricated on a CMOS integrated circuit chip performs parallel intracellular recording from a few hundreds of cardiomyocytes, which marks a new milestone in electrophysiology.
Topics: Animals; B-Lymphocytes; Cell Line; Cell Membrane; Electrodes; Electrophysiological Phenomena; Humans; Myocytes, Cardiac; Nanoparticles; Neurons
PubMed: 29437381
DOI: 10.1021/acs.accounts.7b00519 -
Chemical Science Aug 2023We present an automated droplet reactor platform possessing parallel reactor channels and a scheduling algorithm that orchestrates all of the parallel hardware...
We present an automated droplet reactor platform possessing parallel reactor channels and a scheduling algorithm that orchestrates all of the parallel hardware operations and ensures droplet integrity as well as overall efficiency. We design and incorporate all of the necessary hardware and software to enable the platform to be used to study both thermal and photochemical reactions. We incorporate a Bayesian optimization algorithm into the control software to enable reaction optimization over both categorical and continuous variables. We demonstrate the capabilities of both the preliminary single-channel and parallelized versions of the platform using a series of model thermal and photochemical reactions. We conduct a series of reaction optimization campaigns and demonstrate rapid acquisition of the data necessary to determine reaction kinetics. The platform is flexible in terms of use case: it can be used either to investigate reaction kinetics or to perform reaction optimization over a wide range of chemical domains.
PubMed: 37621435
DOI: 10.1039/d3sc02082g -
Annals of Botany Dec 2023A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups.... (Review)
Review
BACKGROUND
A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes.
SCOPE
The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century.
CONCLUSIONS
The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.
Topics: Animals; Pollination; Phylogeny; Chiroptera; Phenotype; Reproduction; Flowers
PubMed: 37814841
DOI: 10.1093/aob/mcad147 -
Evolution; International Journal of... Apr 2023Species whose ranges encompass substantial environmental variation should experience heterogeneous selection, potentially resulting in local adaptation. Repeated...
Species whose ranges encompass substantial environmental variation should experience heterogeneous selection, potentially resulting in local adaptation. Repeated covariation between phenotype and environment across ecologically similar species inhabiting similar environments provides strong evidence for adaptation. Lesser Antillean anoles present an excellent system in which to study repeated local adaptation because most species are widespread generalists occurring throughout environmentally heterogenous island landscapes. We leveraged this natural replication to test the hypothesis that intraspecific variation in phenotype (coloration and morphology) is consistently associated with environment across 9 species of bimaculatus series anoles. We measured dorsal coloration from 173 individuals from 6 species and 16 morphological traits from 883 individuals from 9 species, spanning their island ranges. We identified striking, but incomplete, parallelism in dorsal coloration associated with annual precipitation in our study species. By contrast, we observed significant patterns of morphological isolation-by-environment in only 2 species and no signal of parallel morphological evolution. Collectively, our results reveal strong divergent natural selection by environment on dorsal coloration but not morphology.
Topics: Animals; Lizards; Adaptation, Physiological; Acclimatization; Phenotype; Selection, Genetic; Biological Evolution
PubMed: 36744479
DOI: 10.1093/evolut/qpad018 -
Central European Journal of Urology 2015Obesity in men is associated with infertility in numerous studies. The current trend for decline in semen parameters parallels the increasing prevalence of obesity... (Review)
Review
INTRODUCTION
Obesity in men is associated with infertility in numerous studies. The current trend for decline in semen parameters parallels the increasing prevalence of obesity worldwide. In addition to impaired semen quality, fertility among obese men may be affected by sexual dysfunction, endocrinopathy, aromatization activity, psychological and thermal effects, sleep apnea, leptin and minor toxins, and possibly the inflammatory and obstructive elements of epididymitis pathology. The variable degrees of certainty associated with these causes parallel the levels of supporting evidence. This search aims to shed lights on different conditions that obese men suffer from; as that makes the treatment of infertility more categorized.
MATERIAL AND METHODS
A PubMed search was conducted to identify clinical and pathological mechanisms linking obesity to male infertility.
RESULTS
Among the myriad of publications reviewed in this paper, impaired spermatogenesis and sexual dysfunction have been shown to drive other variables towards poor fertility potentials. The paper presented a new, detailed flow chart showing more factors and further interactions among conditions leading to infertility.
CONCLUSIONS
The prime hormonal defect in obese men is hypotestosteronaemia, which results in impaired spermatogenesis leading to poor fecundability. Studies have shown that most mechanisms accounting for reduced fertility potentials in overweight men are reversible.
PubMed: 25914843
DOI: 10.5173/ceju.2015.01.435 -
Current Opinion in Lipidology Feb 2022In contrast to other saturated fatty acids, very long-chain saturated fatty acids (VLSFAs) have received limited attention The purpose of this review is to summarize the... (Review)
Review
PURPOSE OF REVIEW
In contrast to other saturated fatty acids, very long-chain saturated fatty acids (VLSFAs) have received limited attention The purpose of this review is to summarize the associations of VLSFAs, including arachidic acid, behenic acid, and lignoceric acid, with cardiovascular disease outcomes and type 2 diabetes; to discuss the findings implications; and to call for future studies of the VLSFAs.
RECENT FINDINGS
Increased levels of circulating VLSFAs have been found associated with lower risks of incident heart failure, atrial fibrillation, coronary heart disease, mortality, sudden cardiac arrest, type 2 diabetes, and with better aging. The VLSFA associations are paralleled by associations of plasma ceramide and sphingomyelin species carrying a VLSFA with lower risks of heart failure, atrial fibrillation, and mortality, suggesting VLSFAs affect the biological activity of ceramides and sphingomyelins thereby impacting health. For diabetes, there is no such parallel and the associations of VLSFAs with diabetes may be confounded or mediated by triglyceride and circulating palmitic acid, possible biomarkers of de novo lipogenesis.
SUMMARY
In many ways, the epidemiology has preceded our knowledge of VLSFAs biology. We hope this review will spur interest from the research community in further studying these potentially beneficial fatty acids.
Topics: Atrial Fibrillation; Cardiovascular Diseases; Ceramides; Diabetes Mellitus, Type 2; Fatty Acids; Heart Failure; Humans
PubMed: 34907969
DOI: 10.1097/MOL.0000000000000806 -
BMC Psychiatry Jun 202322q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal interstitial-deletion disorder, occurring in approximately 1 in 2000 to 6000 live births. Affected...
BACKGROUND
22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal interstitial-deletion disorder, occurring in approximately 1 in 2000 to 6000 live births. Affected individuals exhibit variable clinical phenotypes that can include velopharyngeal anomalies, heart defects, T-cell-related immune deficits, dysmorphic facial features, neurodevelopmental disorders, including autism, early cognitive decline, schizophrenia, and other psychiatric disorders. Developing comprehensive treatments for 22q11.2DS requires an understanding of both the psychophysiological and neural mechanisms driving clinical outcomes. Our project probes the core psychophysiological abnormalities of 22q11.2DS in parallel with molecular studies of stem cell-derived neurons to unravel the basic mechanisms and pathophysiology of 22q11.2-related psychiatric disorders, with a primary focus on psychotic disorders. Our study is guided by the central hypothesis that abnormal neural processing associates with psychophysiological processing and underlies clinical diagnosis and symptomatology. Here, we present the scientific background and justification for our study, sharing details of our study design and human data collection protocol.
METHODS
Our study is recruiting individuals with 22q11.2DS and healthy comparison subjects between the ages of 16 and 60 years. We are employing an extensive psychophysiological assessment battery (e.g., EEG, evoked potential measures, and acoustic startle) to assess fundamental sensory detection, attention, and reactivity. To complement these unbiased measures of cognitive processing, we will develop stem-cell derived neurons and examine neuronal phenotypes relevant to neurotransmission. Clinical characterization of our 22q11.2DS and control participants relies on diagnostic and research domain criteria assessments, including standard Axis-I diagnostic and neurocognitive measures, following from the Measurement and Treatment Research to Improve Cognition in Schizophrenia (MATRICS) and the North American Prodrome Longitudinal Study (NAPLS) batteries. We are also collecting measures of autism spectrum (ASD) and attention deficit/hyperactivity disorder (ADHD)-related symptoms.
DISCUSSION
Studying 22q11.2DS in adolescence and adulthood via deep phenotyping across multiple clinical and biological domains may significantly increase our knowledge of its core disease processes. Our manuscript describes our ongoing study's protocol in detail. These paradigms could be adapted by clinical researchers studying 22q11.2DS, other CNV/single gene disorders, or idiopathic psychiatric syndromes, as well as by basic researchers who plan to incorporate biobehavioral outcome measures into their studies of 22q11.2DS.
Topics: Adolescent; Adult; Humans; Child; Young Adult; Middle Aged; DiGeorge Syndrome; Longitudinal Studies; Psychotic Disorders; Autistic Disorder; Child Development Disorders, Pervasive; Chromosome Deletion
PubMed: 37312091
DOI: 10.1186/s12888-023-04888-5 -
Journal of Bacteriology Oct 2016Microbial adaptation is conspicuous in essentially every environment, but the mechanisms of adaptive evolution are poorly understood. Studying evolution in the... (Review)
Review
Microbial adaptation is conspicuous in essentially every environment, but the mechanisms of adaptive evolution are poorly understood. Studying evolution in the laboratory under controlled conditions can be a tractable approach, particularly when new, discernible phenotypes evolve rapidly. This is especially the case in the spatially structured environments of biofilms, which promote the occurrence and stability of new, heritable phenotypes. Further, diversity in biofilms can give rise to nascent social interactions among coexisting mutants and enable the study of the emerging field of sociomicrobiology. Here, we review findings from laboratory evolution experiments with either Pseudomonas fluorescens or Burkholderia cenocepacia in spatially structured environments that promote biofilm formation. In both systems, ecotypes with overlapping niches evolve and produce competitive or facilitative interactions that lead to novel community attributes, demonstrating the parallelism of adaptive processes captured in the lab.
Topics: Biofilms; Burkholderia cenocepacia; Directed Molecular Evolution; Pseudomonas fluorescens
PubMed: 27044625
DOI: 10.1128/JB.01018-15 -
Annual Review of Physical Chemistry Apr 2022We review a suite of stochastic vector computational approaches for studying the electronic structure of extended condensed matter systems. These techniques help reduce... (Review)
Review
We review a suite of stochastic vector computational approaches for studying the electronic structure of extended condensed matter systems. These techniques help reduce algorithmic complexity, facilitate efficient parallelization, simplify computational tasks, accelerate calculations, and diminish memory requirements. While their scope is vast, we limit our study to ground-state and finite temperature density functional theory (DFT) and second-order many-body perturbation theory. More advanced topics, such as quasiparticle (charge) and optical (neutral) excitations and higher-order processes, are covered elsewhere. We start by explaining how to use stochastic vectors in computations, characterizing the associated statistical errors. Next, we show how to estimate the electron density in DFT and discuss effective techniques to reduce statistical errors. Finally, we review the use of stochastic vectors for calculating correlation energies within the second-order Møller-Plesset perturbation theory and its finite temperature variational form. Example calculation results are presented and used to demonstrate the efficacy of the methods.
Topics: Electronics
PubMed: 35081326
DOI: 10.1146/annurev-physchem-090519-045916 -
Nature Neuroscience Mar 2018Adolescence is a period of social, psychological and biological development. During adolescence, relationships with others become more complex, peer relationships are... (Review)
Review
Adolescence is a period of social, psychological and biological development. During adolescence, relationships with others become more complex, peer relationships are paramount and social cognition develops substantially. These psychosocial changes are paralleled by structural and functional changes in the brain. Existing research in adolescent neurocognitive development has focused largely on averages, but this obscures meaningful individual variation in development. In this Perspective, we propose that the field should now move toward studying individual differences. We start by discussing individual variation in structural and functional brain development. To illustrate the importance of considering individual differences in development, we consider three sources of variation that contribute to neurocognitive processing: socioeconomic status, culture and peer environment. To assess individual differences in neurodevelopmental trajectories, large-scale longitudinal datasets are required. Future developmental neuroimaging studies should attempt to characterize individual differences to move toward a more nuanced understanding of neurocognitive changes during adolescence.
Topics: Adolescent; Adolescent Development; Brain; Child; Culture; Female; Humans; Individuality; Male; Social Class; Young Adult
PubMed: 29403031
DOI: 10.1038/s41593-018-0078-4